Hello all, I am trying to resolve the phylogeny of a bacterial group. Trees infered using conventional approaches based on sequence data are conflicting. Therefore I'm think about using genome rearrangement data to build trees. I first used Mauve to align the genomes and identify the homologous genomic blocks. Then I export the data (permutation matrix) and tried to use other programs to build tree based on it. I'm not interested in rearrangement history, but just focus on species tree. So far I tried MGR, MGRA and BADGER. MGR runs, but veeeeeeerrrry slowly. The latter two programs just don't work for my case. Therefore I am here asking if anyone happens to know some better solutions. Thank you for your time reading this!